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Enable TPI with the Verlet cut-off scheme
2019-03-19
Berk Hess
Reduce dependencies of n
b
n
x
n
_atomdata_t
commit
|
commitdiff
|
tree
2019-03-15
Berk Hess
Change nbnxn_search
to
c
lass PairSearch
commit
|
commitdiff
|
tree
2019-03-15
Berk H
e
ss
Ext
r
act Domain
S
etu
p
from nbnxn_se
a
rch
commit
|
commitdiff
|
tree
2019-03-14
Berk Hes
s
C
hange nbnxm macros to
constexpr
commit
|
commitdiff
|
tree
2019-03-14
Berk He
s
s
Move funct
i
ons to gridset
.
cpp
commit
|
commitdiff
|
tree
2019-03-14
B
e
r
k Hess
Ad
d
n
bnxm Grid
S
et
class
commit
|
commitdiff
|
tree
2019-03-14
Berk Hess
Fix compilation issue
commit
|
commitdiff
|
tree
2019-03-12
Berk
Hess
Move
n
b
nxm atom macros
to ato
m
data
.
h
commit
|
commitdiff
|
tree
2019-03-11
Berk
H
ess
A
dd gromp
p
warning with use of GRO
M
O
S
FF
commit
|
commitdiff
|
tree
2019-03-08
Berk
H
ess
Clean up calc_
v
er
l
et_buffer
_
size()
commit
|
commitdiff
|
tree
2019-03-06
Berk Hess
Clea
n
up n
b
nxm boun
d
i
n
g box fu
n
ctions
commit
|
commitdiff
|
tree
2019-03-06
Berk Hess
Clean up nbnxm bounding boxes
commit
|
commitdiff
|
tree
2019-03-06
B
e
rk Hess
Convert
n
b
n
xm
b
ou
n
ding box to a struct
commit
|
commitdiff
|
tree
2019-03-05
B
erk Hess
Fix po
s
t-submit war
n
ings
commit
|
commitdiff
|
tree
2019-03-05
Berk Hess
Move nbnxm ato
m
d
ata types to
a
to
m
data
.
h
commit
|
commitdiff
|
tree
2019-03-05
Berk
H
ess
Tu
r
n
n
bn
x
n_grid_
t
into a clas
s
commit
|
commitdiff
|
tree
2019-02-28
Berk H
e
ss
Use
u
n
i
q
ue_ptr in nonbon
d
ed_
v
erle
t
_t
commit
|
commitdiff
|
tree
2019-02-27
B
e
rk Hess
Use
ne
w
/delete for t_forcerec
commit
|
commitdiff
|
tree
2019-02-27
Berk Hess
C
le
a
n up
d
is
p
ersi
o
n
c
orrec
t
ion
.
cp
p
commit
|
commitdiff
|
tree
2019-02-27
Berk He
s
s
Fix 4
c
ompiler
s
warnings
commit
|
commitdiff
|
tree
2019-02-27
Berk Hess
C
ollect
di
s
persion correction code
commit
|
commitdiff
|
tree
2019-02-26
Berk Hess
Correct grompp index file error message
commit
|
commitdiff
|
tree
2019-02-26
Ber
k
Hess
Cl
e
an up mtop pb
c
fu
n
c
tions
commit
|
commitdiff
|
tree
2019-02-23
Berk He
s
s
Move all nbnxm pruning details i
n
to mo
d
ule
commit
|
commitdiff
|
tree
2019-02-23
Be
r
k H
e
ss
Hide intern
a
ls of nbnxm pa
r
list
commit
|
commitdiff
|
tree
2019-02-22
Berk Hess
Formal
i
ze dyn
a
mic pruni
n
g
with GP
U
emu
l
a
t
ion
commit
|
commitdiff
|
tree
2019-02-21
Berk Hess
Move fre
e
-energy kerne
l
d
ispatch in
t
o
nbnxm mod
u
le
commit
|
commitdiff
|
tree
2019-02-21
Ber
k
Hes
s
Minor n
b
nxm c
l
eanup
commit
|
commitdiff
|
tree
2019-02-21
Berk
Hess
Clea
n
u
p nbnxm enums
commit
|
commitdiff
|
tree
2019-02-21
B
e
rk Hess
Simplify ma
k
e_pairlist() call
signature
commit
|
commitdiff
|
tree
2019-02-20
B
e
r
k
H
e
ss
A
d
d havePPDomainDecompositi
o
n()
commit
|
commitdiff
|
tree
2019-02-20
Berk Hess
Refac
t
or DLB region h
a
ndl
i
n
g
commit
|
commitdiff
|
tree
2019-02-20
Be
r
k He
s
s
Fix mass Delt
a
H dou
b
le co
u
nt
i
ng
commit
|
commitdiff
|
tree
2019-02-20
Berk Hess
Fix incorrect LJ repulsion fo
r
ce sw
i
tc
h
ing on GPUs
commit
|
commitdiff
|
tree
2019-02-17
Berk He
s
s
Use e
n
um clas
s
fo
r
nb
n
xm local
i
ty
commit
|
commitdiff
|
tree
2019-02-17
Berk Hess
Extract nbnxm
gr
i
d
.
h and pairlistwor
k
.
h
commit
|
commitdiff
|
tree
2019-02-17
Berk Hess
Fix comp
i
ler warnings
commit
|
commitdiff
|
tree
2019-02-17
Berk
Hess
Move
n
bnxm
d
etails from sim_uti
l
.
cpp to module
commit
|
commitdiff
|
tree
2019-02-16
Berk Hess
Move nbnxn files to nbnx
m
directory
commit
|
commitdiff
|
tree
2019-02-15
Be
r
k Hess
Fix
m
ass Delta H double c
o
unting
commit
|
commitdiff
|
tree
2019-02-09
B
e
rk
Hess
Disa
l
low rer
u
n with perturbed masses or cons
t
raints
commit
|
commitdiff
|
tree
2019-02-06
Berk Hess
Fix segf
a
ult
w
ith EM, D
D
a
nd group scheme
commit
|
commitdiff
|
tree
2019-02-01
Berk Hess
F
i
x i
n
cor
r
ect
LJ
r
epul
s
i
o
n force s
w
itching
on
G
P
U
s
commit
|
commitdiff
|
tree
2019-01-25
Berk Hess
Fi
x
LINCS bug f
r
om re
c
e
n
t commit 21
1
0
39fc
commit
|
commitdiff
|
tree
2019-01-23
Berk Hess
Fix e
r
ror with 2D/3
D
DLB
commit
|
commitdiff
|
tree
2019-01-22
Berk Hess
Add ut
i
lity meth
o
d to NbnxnPairlis
t
G
pu
commit
|
commitdiff
|
tree
2019-01-22
Berk Hes
s
R
e
move now usused GPU allo
c
/free funct
i
ons
commit
|
commitdiff
|
tree
2019-01-22
Berk Hess
C
o
nv
e
rt NbnxnPairlistGpu to C
+
+
commit
|
commitdiff
|
tree
2019-01-21
Berk Hess
Co
n
ver
t
nbnxn
_
atomdata_t to C++
commit
|
commitdiff
|
tree
2019-01-16
Berk Hess
Rename HostVector to Padde
d
HostVector
commit
|
commitdiff
|
tree
2019-01-10
Berk Hess
Split nbnxn_atomdata_init()
commit
|
commitdiff
|
tree
2019-01-10
B
e
rk Hess
Ch
a
nge grid poi
n
ter
s
in
nbnxn se
a
rc
h
to refer
e
nc
e
s
commit
|
commitdiff
|
tree
2019-01-10
B
erk Hess
S
pl
i
t nbnxn_l
i
st_
w
ork_t
and c
h
ange to C++
commit
|
commitdiff
|
tree
2019-01-10
Berk Hes
s
Use
s
td::ve
c
tor in Nb
n
xnPairlistCpu
commit
|
commitdiff
|
tree
2019-01-09
Berk
H
ess
Fix gcc-8
r
e
l
ease warnings in
tng
_
io
commit
|
commitdiff
|
tree
2019-01-09
Berk Hess
Added
DefaultInitializationAllocator
commit
|
commitdiff
|
tree
2019-01-04
Berk H
e
ss
Split nbnxn pairlist types for CPU and G
P
U
commit
|
commitdiff
|
tree
2019-01-04
Berk
H
e
s
s
Rep
l
ace NB
N
XN_
C
P
U
_
CLUSTE
R
_
I_SIZE by c
_
nbnxnCpuIClusterSize
commit
|
commitdiff
|
tree
2019-01-03
Berk
H
e
s
s
Fix segmentati
o
n fault in DD code
commit
|
commitdiff
|
tree
2018-12-27
Berk Hess
Use AtomP
a
ir for LINCS indexing
commit
|
commitdiff
|
tree
2018-12-27
Berk Hess
Us
e
a
r
rayref
i
n
LINCS
commit
|
commitdiff
|
tree
2018-12-21
Ber
k
He
s
s
Improve nbnxn cjFromC
i
() func
t
ion
commit
|
commitdiff
|
tree
2018-12-18
Be
r
k Hess
Use s
t
d::vecto
r
in LIN
C
S
commit
|
commitdiff
|
tree
2018-12-14
Berk
H
ess
Fix LINCS trian
g
le
constraining with OpenM
P
commit
|
commitdiff
|
tree
2018-12-14
Be
r
k Hess
Fi
x
ed nullptr de
r
efenc
e
i
n
LINCS error
commit
|
commitdiff
|
tree
2018-12-14
Be
r
k Hess
Fi
x
LINCS triangle cons
t
r
a
ining with Ope
n
MP
commit
|
commitdiff
|
tree
2018-12-12
Berk Hess
T
e
m
porary fix for OpenCL PME
g
ather
commit
|
commitdiff
|
tree
2018-12-11
B
e
rk He
s
s
Fix
updat
e
groups with
2
D/3D DLB
commit
|
commitdiff
|
tree
2018-12-11
Be
r
k Hes
s
Make large PME grids work
o
n
GPU
commit
|
commitdiff
|
tree
2018-12-11
Berk Hess
Docum
e
nt m
d
run mdp
opti
o
n mo
d
i
fication
commit
|
commitdiff
|
tree
2018-12-05
Berk Hess
Add upda
t
e
grou
p
s to p
a
ralleliz
a
tion docs
commit
|
commitdiff
|
tree
2018-12-05
Be
r
k Hess
Make large P
M
E grids wor
k
on
G
PU
commit
|
commitdiff
|
tree
2018-11-26
Berk Hess
F
ix FP exception in pul
l
c
o
de
commit
|
commitdiff
|
tree
2018-11-16
Berk Hess
gr
o
mpp now checks tau-p
>
=2*tau-t with N
H
+P
R
commit
|
commitdiff
|
tree
2018-11-08
B
erk Hess
Fix
bug w
i
t
h DD fo
r
d
ims without
P
B
C
commit
|
commitdiff
|
tree
2018-11-01
Berk Hess
Fix broken u
p
date
groups
commit
|
commitdiff
|
tree
2018-10-31
Berk H
e
ss
Lim
i
t auto assignment of bonded
s
t
o
GPUs
commit
|
commitdiff
|
tree
2018-10-31
Berk
H
ess
Pin i
m
port
a
n
t
b
uffers in CUDA b
o
ndeds
commit
|
commitdiff
|
tree
2018-10-31
B
e
rk He
s
s
Work
a
roun
d
e
x
p
and
e
d ensemble issues
commit
|
commitdiff
|
tree
2018-10-31
Berk Hess
Fix FP exception
in ene
r
g
y
reduction
commit
|
commitdiff
|
tree
2018-10-31
Berk Hess
C
orrect VV i
n
tegrator
n
stcalc
e
ner
g
y use
commit
|
commitdiff
|
tree
2018-10-31
Ber
k
Hes
s
C
orrect grompp nstexp
a
nded/
n
s
tcalce
n
ergy
check
commit
|
commitdiff
|
tree
2018-10-26
Berk Hess
Add missing mass
term
t
o d
e
ltaH
commit
|
commitdiff
|
tree
2018-10-23
B
e
r
k He
s
s
Add
m
i
s
sing constraint term to deltaH
commit
|
commitdiff
|
tree
2018-10-21
B
erk H
e
s
s
Fix
m
d
run start/end t
i
me prin
t
commit
|
commitdiff
|
tree
2018-10-18
B
e
rk Hess
Add
env
.
v
a
r
.
to disa
b
le u
p
date gro
u
ps
commit
|
commitdiff
|
tree
2018-10-12
B
erk He
s
s
Implement ass
i
gning bondeds
t
o the GP
U
commit
|
commitdiff
|
tree
2018-10-10
Berk
Hess
Move pull ou
t
p
u
t functions to o
u
tput
.
cpp
commit
|
commitdiff
|
tree
2018-10-10
Berk
H
ess
Mino
r
refac
t
ori
n
g in b
o
nded
t
h
reading
commit
|
commitdiff
|
tree
2018-10-09
Berk Hess
Fix com
p
iler wa
r
ni
n
g
commit
|
commitdiff
|
tree
2018-10-08
Berk Hess
Enable update groups
commit
|
commitdiff
|
tree
2018-10-05
Berk H
e
ss
Add
u
pd
a
te groups to DD atom di
s
placement
commit
|
commitdiff
|
tree
2018-10-04
Berk Hess
Mak
e
A
V
X2 pass TSAN
commit
|
commitdiff
|
tree
2018-10-04
Berk Hess
Add note to avoi
d
c
o
nstraint
s
=
al
l
-bonds
commit
|
commitdiff
|
tree
2018-10-03
Berk
Hess
R
emov
e
u
n
necessary
c
leari
n
g
in
g
mxcpp
commit
|
commitdiff
|
tree
2018-10-03
Berk
H
e
ss
C
onvert gmx_c
p
p
t
o
C++
commit
|
commitdiff
|
tree
2018-10-02
Berk
H
ess
Update DD cutoffs f
o
r up
d
ate
groups
commit
|
commitdiff
|
tree
2018-09-30
Berk Hess
Correct up
d
a
te group angle param type
commit
|
commitdiff
|
tree
2018-09-29
Be
r
k Hess
Refacto
r
ing in calc_verletbuf
.
cp
p
commit
|
commitdiff
|
tree
2018-09-29
Berk Hes
s
Ad
d
UpdateGroupsCog to DD
commit
|
commitdiff
|
tree
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